Postdoc in machine learning applied to gene regulation, France

Position title: Postdoc in machine learning applied to gene regulation

Employer: CNRS

Closing date: 1/3/2019

Brief position description: A two-year postdoctoral position is available in the machine learning and gene regulation group directed by William Ritchie at the Institut de Génétique Humaine in Montpellier, South of France. The IGH is a world leader in the field of gene regulation, with state-of-the art facilities and teams of international renown.

Our group uses machine learning approaches to integrate omics data to understand normal biology and disease. We have a strong background in applying novel algorithmic approaches to better understand mechanisms of gene expression and RNA processing (Middleton et al., Genome Biology, 2017; Wong et al., Nature Comms, 2017; Wong et al., Cell, 2013).

We have currently generated a wealth of transcriptomic data (mRNA-seq, ONT long-read seq) and epigenetic data to dissect the epithelial to mesenchymal transition underlying tumor progression and metastasis. We will integrate this data as well as explore long range interactions that may regulate RNA processing through direct contact with enhancers. 

We are therefore looking for very motivated, hard-working and creative candidates with strong background in computer science or statistics to explore RNA regulation through epigenetic and long range interactions. Previous expertise in RNA processing and/or epigenetics will be positively evaluated.

Job website: http://www.igh.cnrs.fr/en/about-igh/job-opportunities/320-postdoc-machine-learning-applied-to-transcriptomic-data-in-a-model-of-metastasis-hf

Contact name: william ritchie

Contact email: william.ritchie@igh.cnrs.fr

Research Officer – Bioinformatics of Speech Disorders, Melbourne

Position title: Research Officer – Bioinformatics of Speech Disorders

Employer: Walter and Eliza Hall Institute of Medical Research

Closing date: 5:00pm, Friday 1st March 2019

Brief position description: An opportunity exists for a Research Officer specialising in the genetics of speech disorders to join the Bahlo laboratory. The successful candidate will join an international collaboration between speech pathologists, geneticists, imaging and bioinformatics experts.

About the position:
The appointee will undertake bioinformatics analyses of genetic data generated for family and cohort studies in speech disorders, interacting with genetic, clinical and imaging experts involved in understanding the speech phenotypes in the patients. The data will be primarily next generation sequencing data from whole-exome, whole-genome sequencing or targeted sequencing of cohort and family-based studies. The research officer will oversee several exciting studies, analysing data, analysing and managing the research outcomes from these projects. The research officer will also integrate with other work in the Bahlo laboratory to apply novel methods for prioritisation of putative speech disorder candidate genes, which can be assessed in large national and international cohorts. The work is highly likely to lead to high-impact publications with the expectation of presentations at national and international conferences. The research officer will use advanced bioinformatics tools developed at the WEHI and elsewhere and will have access to high quality computing facilities.

Selection Criteria:
Applicants with a PhD in a relevant discipline are welcome to apply. Relevant disciplines include computer science, mathematics, statistics, computational biology or genetics. Applicants need to have extensive experience in the analysis of next generation sequencing data and a good understanding of genetics with a proven research track record of publications. Experience in speech disorder genetic research is desirable, but not essential. The position requires high-level project-management skills, strong programming and data analysis skills and, in particular strong communication skills to ensure excellent communication as a key person working between the two laboratories.

Terms of appointment: 
The positions will be for 2 years in the first instance. Salary is dependent upon qualifications and experience. Up to 17% superannuation and attractive salary packaging options are available.

Job website: http://www.wehi.edu.au/research-officer-%E2%80%93-bioinformatics-speech-disorders

Contact name: Melanie Bahlo

Contact email: bahlo@wehi.edu.au

Biostatistician, Sydney

• Opportunity to provide statistical analysis to the Prevention Research Collaboration, a research group of the Sydney School of Public Health, Faculty of Medicine and Health

• Located at Charles Perkins Centre within the Camperdown Campus

• Full-time, fixed term for 3 years with a base salary of $104-123k pa plus superannuation

About the opportunity

The Prevention Research Collaboration (PRC) is a research group within the Sydney School of Public Health, at the University of Sydney and has specialised expertise in population-wide prevention research and translational research.

The Biostatistician will use their advanced knowledge of quantitative methods and analytical skills to conduct relevant statistical work and support research within the PRC, and more specifically in support of research activities auspiced by NSW Health Prevention Research Support Program (PRSP) and the NSW Research Program for Physical Activity, Nutrition and Obesity Prevention (RPANOP).

About you

The University values courage and creativity; openness and engagement; inclusion and diversity; and respect and integrity. As such, we see the importance of recruiting talent aligned to these values and are looking for a high potential Biostatistician who possess:

• relevant tertiary qualifications in statistics or biostatistics

• experience in health-related statistical analysis with demonstrated skills in applying advanced

  methods (e.g., multivariate modelling including GEE and related techniques), and other

  relevant software packages (e.g., SAS, STATA or SPSS or equivalent)

• experience in multivariate modelling relevant to public health and experience in calculating

  complex sample sizes and weighting in population health studies

• experience in analysing routine surveillance and population health data, and intervention data

• demonstrated skills in data management and analysis of health and intervention data.

The successful candidate will use their effective communication skills to understand technical information and translate this to different audiences both internally and externally, as well as, maintain high work standards with minimal guidance and supervision.

About us

For more information regarding The Prevention Research Collaboration (PRC) please visit:

http://sydney.edu.au/medicine/public-health/prevention-research/

Since our inception 160 years ago, the University of Sydney has led to improve the world around us. We believe in education for all and that effective leadership makes lives better. These same values are reflected in our approach to diversity and inclusion, and underpin our long-term strategy for growth. We’re Australia's first university and have an outstanding global reputation for academic and research excellence. Across our campuses, we employ over 7600 academic and non-academic staff who support over 60,000 students.

We are undergoing significant transformative change which brings opportunity for innovation, progressive thinking, breaking with convention, challenging the status quo, and improving the world around us.

How to apply

For more information on the position and University, please view the candidate information packavailable from the job’s listing on the University of Sydney careers website.

All applications must be submitted via the University of Sydney careers website. 

Visit sydney.edu.au/recruitment and search by the reference number 119/0119F to apply.

Closing date: 11:30pm, 25 February 2019

Please note: visa sponsorship is not available for this position

The University of Sydney is committed to diversity and social inclusion. Applications from people of culturally and linguistically diverse backgrounds; equity target groups including women, people with disabilities, people who identify as LGBTIQ; and people of Aboriginal and Torres Strait Islander descent, are encouraged.

© The University of Sydney
The University reserves the right not to proceed with any appointment.

Junior & Senior Bioinformaticians, Sydney

Position title: Junior & Senior Bioinformaticians

Employer: Garvan Institute of Medical Research

Closing date: The position will remain open until filled. As we will be reviewing applications as they are received, we encourage you to submit yours as soon as possible.

Brief position description: Established by the Garvan Institute in 2012, the Kinghorn Centre for Clinical Genomics (KCCG) advances the use of genomic information in patient care. KCCG acts as a mechanism to translate genomic research information into patient care. To do this KCCG employs experts in genomics including researchers, bioinformaticians, clinicians, educators and software engineers. We use world-leading OMICS based technology to enhance diagnosis and treatment for patients. 

KCCG is integrated with numerous state and nationwide flagship genomic research projects, and partners with many national and international collaborative organisations and funding bodies. 

The Translational Genome Informatics Group (TIG) within KCCG is a multidisciplinary team of bioinformaticians, statisticians, software engineers and clinical researchers, developing and deploying bioinformatic methods to study genomic variation, focussed on particular diseases. This work includes rare monogenic disease and cancer as well as complex diseases such as diabetes, osteoporosis and immunological immune diseases. 

This position will work with the team leader of the Translational Genome Informatics Group to perform research into translational genomics, including developing, streamlining, and validating approaches for analysing and interpreting multi-omic data with the focus on clinical translation.

The role will be responsible for developing new bioinformatic approaches to study unique aspects of various diseases, and incorporate these into the analytical pipeline. These methods should be developed in a manner consistent with KCCG’s development practices, so that they can be translated into the clinical pipeline. There is scope within this position to perform genomics and bioinformatics research, publish scientific papers, and to pursue independent funding. 

The Opportunity

Reporting to the Head of Translational Genomics, this position will be responsible for helping to provide direction and support in clinical genomics, genome informatics and translational research in cancer genomics. This will include: 

• Undertaking and directing translational research with an emphasis on developing biological insights that are relevant to patient outcomes.
• Improve the breadth, quality and efficiency of existing genomic analysis pipelines, through development of improved bioinformatics approaches.
• Develop approaches to optimise and streamline interpretation of genomes.
• Day-to-day support and occasional training of students and junior staff as required.
• Occasionally represent KCCG at events, or talks with external stakeholders.
• Staying abreast on advances in genomics and next generation sequencing technology in general as well as maintaining knowledge about clinical genomic testing and personalised medicine.

The position will be offered full-time for 2 years in the first instance.

 
About You

• PhD degree in a related area of science, or equivalent, or Master’s degree with at least 3 years of experience 
• Significant postdoctoral or industry experience in related disciplines (for senior role)
• Highly developed skills in bioinformatics and genomics
• Strong expertise in working with next-generation sequencing data
• Ability to develop, manage and maintain internal and external relationships
• Highly developed written and verbal communications skills
• Project management skills 

Desired
• Strong expertise in clinical interpretation of genomic data
• Software engineering skills: source control management, unit and regression testing, continuous integration 
• Expertise in developing diagnostic assays, and assessing their analytical performance

How to Apply 

All applications must be submitted via the Garvan Careers site via the link below. Applications from other sites/channels will unfortunately not be considered.

https://garvan.applynow.net.au/jobs/GC201924 

Your application should include: 
• A cover letter
• Your resume including at least 2 referees
• Copies of relevant qualifications / academic transcripts

Only applicants with working rights in Australia are eligible to apply for this role.

Job website: https://garvan.applynow.net.au/jobs/GC201924

Contact name: Kim Ooi

Contact email: hr@garvan.org.au

Clinical Bioinformatician, NSW

Position title: Clinical Bioinformatician

Employer: NSW Health Pathology/Mackenzie’s Mission and CRE in Neurocognitive Disorders (CRE-NCD)

Closing date: 1st March, 2019

Brief position description: The NSW Health Pathology Randwick Genetics Laboratory is one of the major Australian centres for genetic diagnostics, providing a comprehensive genome diagnostic service in a consultative pathology context. The laboratory is recognised as a training site by both the HGSA and RCPA for advanced training in laboratory genetics for both scientific and medical personnel. NSW Health Pathology Randwick Genetics Laboratory has held continuous accreditation from NATA/RCPA since 1988, providing testing compliant with the ISO 15189 and ISO 9001 Standards and NPAAC Requirements. 
Mackenzie's Mission is a large-scale reproductive carrier screening pilot study which will screen 10,000 couples across Australia for ~500 rare and debilitating genetic disorders including spinal muscular atrophy (SMA), fragile X syndrome and cystic fibrosis (CF).
The CRE-NCD, based at Neuroscience Research Australia, is a five year-funded NHMRC centre that aims to transform the diagnosis and management of intellectual disability (also known as neurocognitive disorders) through whole exome sequencing (WES) and whole genome sequencing (WGS). 
This position will support the molecular genetics laboratory, Mackenzie's Mission and the CRE-NCD by assisting with clinical bioinformatics requirements for the analysis of next generation sequencing (NGS) data, implementation and maintenance of pipelines around design, performance, validation and quality control. The clinically targeted NGS panels, exomes or genomes and bioinformatics pipelines require embedded bioinformatic expertise. The ability to perform NGS data analysis using computer programming and Unix-based servers is required. The successful candidate will be working closely with wet lab scientists, clinicians and pathologists, genomic analysts, and other bioinformaticians/software developers.
We are seeking an experienced and motivated Bioinformatician interested in applying their skills in a clinical setting and able to work both independently and as part of a team. This is a full time position, fixed term three years.
For further information about this opportunity, please review the position description or contact us for a confidential discussion.

Job website: https://www.seek.com.au/job/38062803?searchrequesttoken=a3f93400-9a4f-45dc-a1f8-ed211d898bb5&type=standard

Contact name: Tony Roscioli

Contact email: Tony.Roscioli@health.nsw.gov.au

Contact name: Edwin Kirk

Contact email: Edwin.kirk@health.nsw.gov.au

Bioinformatician (Research Officer), Melbourne

Position title: Bioinformatician (Research Officer)

Employer: Murdoch Children's Research Institute

Closing date: 08/02/19

Brief position description: We are seeking a Full Time Research Officer/Postdoc (on a 2.5 Year contract) with strong experience in bioinformatics and a passion for understanding the genetics of rare disease. The role will be focused on the generation, analysis and interpretation of genomic and transcriptomic data from cohorts of individuals with rare genetic disorders. The successful applicant will join the join the Translational Bioinformatics group led by Dr Cas Simons, and work in collaboration with clinicians from the Victorian Clinical Genetics Service, the Royal Children’s Hospital, and national and international collaborators.

The position will be responsible for the analysis of whole genome, exome and transcriptomic data with the aim to establish the molecular basis of rare genetic disorders. 

To be successful in this role you will have:

- PhD in genomics, computational biology, bioinformatics, molecular biology, or a related discipline, with significant computational components
- Substantial experience in the analysis and interpretation of next-generation sequence data
- Evidence of advanced programming skills in Python and BASH
- Experience with version control (e.g. Git, Mercurial) and high-performance computing environments (e.g. PBS, SLURM)
- Evidence of well-developed written and verbal communication skills, for example in academic publications and conference presentations
- Proven ability to work effectively as part of a team to develop and complete research tasks, as well as the motivation and discipline to carry out autonomous research

Salary Range: $90,912 - $97,585 per annum plus super
Position Reference: 15380

Job website: http://career10.successfactors.com/career?company=C0007531036P&career_job_req_id=15380&career_ns=job_listing&navBarLevel=JOB_SEARCH

Contact name: Cas Simons

Contact email: cas.simons@mcri.edu.au

Bioinformatician (Research Officer), Melbourne

Position title: Bioinformatician (Research Officer)

Employer: Murdoch Children's Research Institute

Closing date: 08/02/19

Brief position description: We are seeking a Full Time Research Officer/Postdoc (on a 2.5 year contract) with strong experience in bioinformatics and a passion for understanding the genetics of rare disease. The role will be focused on the generation, analysis and interpretation of genomic and transcriptomic data from cohorts of children with neurodevelopmental disorders, including epilepsy, brain malformations and leukodystrophies. The position will be responsible for developing NGS analysis pipelines, as well as analysis of sequencing data and biological interpretation of results. The successful applicant will join the Translational Bioinformatics group led by Dr Cas Simons, and work as part of the new neurodevelopmental flagship at the MCRI in collaboration with paediatric neurologists A/Prof Richard Leventer and Dr Katherine Howell from the Royal Children’s Hospital and MCRI Neurosciences Research Group, and A/Prof Paul Lockhart from the MCRI Neurogenetic Research Group. In addition to research activities, the successful applicant will have opportunities to interface with clinicians, and patients and gain exposure to clinical tools such as magnetic resonance imaging, by being based within a research group composed of members from all sectors of the Melbourne Children’s Campus.

To be successful in this role you will have:
- PhD in genomics, computational biology, bioinformatics, molecular biology, or a related discipline
- Substantial experience in the analysis and interpretation of next-generation sequence data and an interest in neurodevelopmental disorders
- Demonstrated understanding of Mendelian disorders and a deep understanding of the underlying genetic and biological concepts
- Evidence of advanced programming skills in Python and BASH
- Evidence of well-developed written and verbal communication skills, for example in academic publications and conference presentations
- Proven ability to work effectively as part of a team to develop and complete research tasks, as well as the motivation and discipline to carry out autonomous research

Salary Range: $90,912 - $97,585 per annum plus super
Closing Date: 5pm Friday 8 February 2019
Position Reference: 15892

Job website: http://career10.successfactors.com/career?career%5fns=job%5flisting&company=C0007531036P&navBarLevel=JOB%5fSEARCH&rcm%5fsite%5flocale=en%5fGB&career_job_req_id=15892&selected_lang=en_GB&jobAlertController_jobAlertId=&jobAlertController_jobAlertName=&_s.crb=NaoaVbSHCpDmpuu7pKm%2fZ3gmaM0%3d

Contact name: Cas Simons

Contact email: cas.simons@mcri.edu.au

Research Associate - Bioinformatics Officer, Perth

Employer: University of Western Australia

Closing date: 31st January 2019

Brief position description: The Cancer Research Trust (http://cancerresearchtrust.org.au) has recently funded a 9 year program to enable single cell approaches to study tumour biology. The program led by Professor Alistair Forrest at the Harry Perkins Institute of Medical research is based in Perth Western Australia and is a collaboration involving all of the major hospitals, medical research institutes and Universities in the region.

Seeking to employ a postdoctoral researcher with a PhD at the time of appointment (or equivalent experience) in bioinformatics, computer science, biostatistics, molecular biology or a related discipline with an emphasis in the specific fields of bioinformatics, genomics and systems biology. The candidate will be working directly with Prof Forrest and his team on analysis of single cell datasets.

Essential selection criteria:
• Demonstrated capacity to analyse NGS data, form hypotheses, test them and follow through to publications.
• Experience in documenting, testing and reusing code.
• Proficiency with R or other languages.
• Experience in cancer biology and analysis of single cell data is a bonus.

Job website: http://external.jobs.uwa.edu.au/cw/en/job/502428/research-associate-bioinformatics-officer

Contact name: Alistair Forrest

Contact email: alistair.forrest@perkins.uwa.edu.au

Research Assistant - Bioinformatics & Cellular Genomics, Melbourne

Employer: St Vincent's Institute (SVI)

Closing date: 3 Feb 2019

Brief position description: The Facility 

St Vincent’s Institute (SVI) www.svi.edu.au is an internationally recognised independent research organization, based on the St Vincent’s Hospital Campus on the edge of Melbourne’s CBD. The Institute has a dedicated team of over 150 talented research staff and students, who are committed to improving the health and life-expectancy of Australians. We focus on common diseases that represent major health issues for Australians today, including diabetes, bone diseases, cancer, cardiovascular disease, obesity and Alzheimer’s disease. 

The Laboratory 

The Bioinformatics & Cellular Genomics Laboratory is a newly funded group at SVI, established to solve the challenges of analysing and interpreting the large-scale biological data generated from medical research activity. In a jointly funded arrangement between SVI and the Melbourne Integrative Genomics Group (University of Melbourne School of Mathematics and Statistics) and under the direction of NHMRC Fellow and Oxford graduate Dr Davis McCarthy, the Bioinformatics & Cellular Genomics Laboratory will be capable of using large-scale studies of DNA and single-cell genetics to drive future medical discoveries. 

The Position 

We are seeking a talented Research Assistant to support the single-cell genetics research of the laboratory. Playing a key role alongside the senior scientists, you will carry out a range of supervised work activities across a variety of projects using computational methods, approaches, and software to enable single-cell genetics research. 

The successful incumbent will have an Honours Degree in a computational discipline relevant to bioinformatics and cellular genomics (bioinformatics, statistics, machine learning, computer science, applied mathematics, physics or similar) and have proficiency in one or more of R, Python, C++, Go, Nim, Rust, Java, Perl and/or SQL computer programming and scripting languages. You will have a demonstrated ability in the use of Unix-based systems, computing clusters and related queueing systems and experience in data analysis and management. 

Ideally you will have prior experience working in a high-performance computing environment where you have developed expertise in statistics and/or machine learning. Prior exposure to research in genomics (ideally single-cell genomics), genetics, computational biology or bioinformatics will enhance your success in the role. Exposure to the statistical analysis of large-scale human and/or mouse genomic datasets will be highly regarded. 

Salary: $70,000 - $80,000 per annum, commensurate with qualifications and experience, plus: 

- 9.5% superannuation 

- generous $15,900 FBT exempt salary packaging Position Description - see job website link below

Applications: via Seek please. Please include current CV, covering letter addressing key selection criteria based on the Position Description

Position Enquiries: Dr Davis McCarthy dmccarthy@svi.edu.au

Job website: https://www.svi.edu.au/careers_students/careers/current_vacancies/

Contact name: Helen Ritchie

Contact email: hritchie@svi.edu.au

Post Doctoral Research Officer - Bioinformatics & Cellular Genomics (Melbourne)

Employer: St Vincent's Institute (SVI)

Closing date: 3 Feb 2019

Brief position description: 

The Facility

St Vincent’s Institute (SVI) www.svi.edu.au is an internationally recognised independent research organization, based on the St Vincent’s Hospital Campus on the edge of Melbourne’s CBD. The Institute has a dedicated team of over 150 talented research staff and students, who are committed to improving the health and life-expectancy of Australians. We focus on common diseases that represent major health issues for Australians today, including diabetes, bone diseases, cancer, cardiovascular disease, obesity and Alzheimer’s disease. 

The Laboratory 

The Bioinformatics & Cellular Genomics Laboratory is a newly funded group at SVI, established to solve the challenges of analysing and interpreting the large-scale biological data generated from medical research activity. In a jointly funded arrangement between SVI and the Melbourne Integrative Genomics Group (part of Melbourne University School of Mathematics and Statistics) and under the direction of NHMRC Fellow and Oxford graduate Dr Davis McCarthy, the Bioinformatics & Cellular Genomics Laboratory is capable of using large-scale studies of DNA and single-cell genetics to drive future medical discoveries. 

The Position 

We are seeking a motivated and successful postdoctoral Researcher to manage an independent project in single-cell genetics, developing new computational methods and open-source software to enable cloud-scale analyses of single-cell data. You will implement statistical and machine learning approaches and coordinate the processing and analysis of ‘omic data, identifying opportunities to customise more efficient workflows and methods where warranted. The position also plays an important role in the overall performance and scientific activities of the laboratory as you will contribute to publications, assist in the supervision of students and present at seminars and lab meetings. The researcher will also have an organisation-wide responsibility in collaborating closely with the researchers of the wet-lab laboratories, providing computational expertise on experimental design and data analysis. 

The successful incumbent will have a PhD (or equivalent) in a computational discipline relevant to bioinformatics and cellular genomics (bioinformatics, statistics, machine learning, computer science, applied mathematics, physics or similar) and possess advanced skills in using computer programming and scripting in R or Python and, ideally, familiarity with one or more of C++, Go, Nim, Rust, Java, Perl or SQL programming languages. You will have a demonstrated ability in the use of Unix-based systems, computing clusters and related queueing systems and in large-scale data analysis and management. Ideally you will have prior experience working in high-performance computing environments, including academic and/or commercial cloud computing platforms and experience using bioinformatics workflow management software (e.g. Snakemake, Nextflow, CWL). Your track record in bioinformatics, genomics, computational biology or other relevant quantitative fields will be evidenced by high-quality publications. Demonstrated experience developing open-source software and reproducible data analyses will be highly regarded. 

Salary - commensurate with qualifications and experience, $83,000 - $90,000 pa plus:

• 9.5% superannuation
• generous $15,900 FBT exempt salary packaging

Position Description - see job website listing below

Applications - via Seek please. Include current CV, covering letter addressing selection criteria, based on Position Description

Enquiries - Dr Davis McCarthy dmccarthy@svi.edu.au

Job website: https://www.svi.edu.au/careers_students/careers/current_vacancies/

Contact name: Helen Ritchie

Contact email: hritchie@svi.edu.au